Politician uddhav thackeray biography- Full Details
отчет корона
1. SARS-CoV-2 variants of concern and
variants under investigation in
England
Omicron VOC-21NOV-01 (B.1.1.529)
update on cases, S gene target failure
and risk assessment
8 December 2021
2. 2
SARS-CoV-2 variants of concern and variants under investigation in England: Omicron update
Omicron VOC-21NOV-01 (B.1.1.529)
A new variant with a novel combination of mutations was detected on GISAID on 23
November and designated B.1.1.529 on 24 November. This variant was designated
VUI-21NOV-01 by the UK Health Security Agency (UKHSA) Variant Technical Group and on
review re-designated as VOC-21NOV-01 on 27 November 2021.
Cases of Omicron, VOC-21NOV-01 (B.1.1.529) in
England
Confirmed Omicron VOC-21NOV-01 (B.1.1.529) cases are those which have been identified
by sequencing or genotyping. Additional cases are under investigation.
The Omicron VOC-21NOV-01 (B.1.1.529) genome also contains the spike deletion at
position 69-70 which is associated with S gene target failure (SGTF) in some widely used
polymerase chain reaction (PCR) tests. Such PCR tests evaluate the presence of 3 SARS-
CoV-2 genes: Spike (S), N and ORF1ab. SGTF is defined as a PCR test where the N and
ORF1ab genes are detected (with Ct values <=30) but the S gene is not. SGTF patterns can
be used to assess the spread of Omicron VOC-21NOV-01 (B.1.1.529).
Trends in S gene target failure
Until the week beginning 23 November 2021, the weekly count of cases with S gene target
failure (SGTF) was less than 150, making up less than 0.1% of all cases. Analyses of
sequenced SGTF samples has indicated that until mid-November, more than 99% of these
were Delta cases.
In the most recent week of data (specimen dates from 30 November 2021 reported as of 6
December), the number of cases with SGTF has increased notably to 705 (Figure 1). The
majority of these cases are located in London and the South East (Figure 2).
Trends in SGTF over space and time are however affected by the coverage of laboratories
contributing to this surveillance data. Currently, SGTF monitoring is based on data submitted
by 4 laboratories: Alderley Park, Glasgow, Milton Keynes, and Newcastle Lighthouse
Laboratories. Coverage of these laboratories is particularly low in the South West, which is a
partial explanation for the low numbers of cases with SGTF seen in this region.
3. SARS-CoV-2 variants of concern and variants under investigation in England: Omicron update
3
Figure 1. Coverage of TaqPath laboratories over time and by local authority, England as of 6 December 2021 (1 September
to 2020 to 5 December 2021)
4. SARS-CoV-2 variants of concern and variants under investigation in England: Omicron update
4
Figure 2. Weekly coronavirus (COVID-19) cases with detectable S gene or SGTF among those tested in TaqPath Labs, by
region of residence as of 6 December 2021 (3 August 2021 to 5 December 2021)
5. SARS-CoV-2 variants of concern and variants under investigation in England: Omicron update
5
Omicron cases by local authority
The number of Omicron cases confirmed through sequencing or genotyping in England as of
6 December 2021 was 333. This includes provisional sequencing results (those awaiting
confirmation and addition to CLIMB). These results are used to expedite case identification
for public health response purposes, but are added to United Kingdom figures only once they
are confirmed.
As of 6 December, 295 confirmed cases have been identified with specimen dates in the
most recent 2 weeks (22 November to 5 December). The local authorities with the highest
number of cases in this time period are West Northamptonshire, Croydon, Hackney Lambeth
and Newham.
Table 1. Number of confirmed* Omicron cases and SGTF cases** for 10 local
authorities with highest Omicron case counts in England for most recent 2 weeks
(22 November to 5 December)
Lower-tier local
authority
Region Confirmed
* Omicron
cases (22
November
2021 to 28
November
2021)
SGTF
cases** (22
November
2021 to 28
November
2021)
Confirmed*
Omicron
cases (29
November
2021 to 5
December
2021)
SGTF
cases** (29
November
2021 to 5
December
2021)
West
Northampton-
shire
East
Midlands
10 1 17 55
Croydon London 3 0 5 2
Hackney London 3 0 5 6
Lambeth London 3 0 5 8
Newham London 3 0 5 14
Brent London 5 0 2 7
Buckingham-
shire
South
East
2 0 5 15
Greenwich London 2 0 5 9
Lewisham London 4 1 3 18
Wandsworth London 4 1 2 6
*Confirmed through sequencing, provisional sequencing, and genotyping
**SGTF cases that have been identified to be Omicron or ruled out as other variants not
included
Risk assessment
An updated risk assessment for Omicron VOC-21NOV-01 has been published.
6. SARS-CoV-2 variants of concern and variants under investigation in England: Omicron update
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Sources and acknowledgments
Data sources
Data used in this investigation is derived from the COG-UK and UKHSA genomic
programme data set, the UKHSA Second Generation Surveillance System (SGSS), the
Secondary Uses Service (SUS) data set, Emergency Care Data Set (ECDS), and the
UKHSA Case and Incident Management System (CIMS). Data on international cases is
derived from reports in GISAID.
Repository of human and machine-readable
genomic case definitions
Genomic definitions for all VOC and VUI are provided in order to facilitate standardised VOC
and VUI calling across sequencing sites and bioinformatics pipelines and are the same
definitions used internally at UKHSA. Definition files are provided in YAML format so are
compatible with a range of computational platforms. The repository will be regularly updated.
The genomic and biological profiles of VOC and VUI are also detailed on first description in
prior technical briefings.
Variant Technical Group
Authors of this report
UKHSA Genomics Cell
UKHSA Outbreak Surveillance Team
UKHSA Epidemiology Cell
UKHSA Contact Tracing Data Team
UKHSA International Cell
UKHSA Environmental Monitoring for Health Protection Team
Contributions from the Variant Technical Group Members
Variant Technical Group members and contributors
The UK Health Security Agency Variant Technical Group includes members and contributors
from the following organisations: UKHSA, Public Health Wales, Public Health Scotland,
7. SARS-CoV-2 variants of concern and variants under investigation in England: Omicron update
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Public Health Agency Northern Ireland, the Department of Health and Social Care, Imperial
College London, London School of Hygiene and Tropical Medicine, University of
Birmingham, University of Cambridge (including the MRC Biostatistics Unit), University of
Edinburgh, University of Liverpool, the Wellcome Sanger Institute, Genotype to Phenotype
Consortium, SPI-M.
Acknowledgements
The authors are grateful to those teams and groups providing data for these analyses
including: the Lighthouse Laboratories, NHS, COG-UK, the Wellcome Sanger Institute,
Health Protection Data Science teams, the Joint Biosecurity Centre and the Genotype to
Phenotype Consortium.
